› 2zke

X-ray diffraction
2.6Å resolution

Crystal structure of the SRA domain of mouse Np95 in complex with hemi-methylated CpG DNA

Released:
DOI: 10.2210/pdb2zke/pdb
PDB entry 2zke coloured by chain, front view.
PDB entry 2zke coloured by chain, side view.
PDB entry 2zke coloured by chain, top view.
Source organism: Mus musculus
Primary publication:
Recognition of hemi-methylated DNA by the SRA protein UHRF1 by a base-flipping mechanism.
Arita K, Ariyoshi M, Tochio H, Nakamura Y, Shirakawa M
Nature 455 818-21 (2008)
PMID: 18772891

Function and Biology Details

Reaction catalysed: 
S-ubiquitinyl-[E2 ubiquitin-conjugating enzyme]-L-cysteine + [acceptor protein]-L-lysine = [E2 ubiquitin-conjugating enzyme]-L-cysteine + N(6)-ubiquitinyl-[acceptor protein]-L-lysine
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-115968 (preferred)
Entry contents:
1 distinct polypeptide molecule
2 distinct DNA molecules
Macromolecules (3 distinct):
E3 ubiquitin-protein ligase UHRF1 Chain: A
Molecule details ›
Chain: A
Length: 210 amino acids
Theoretical weight: 23.41 KDa
Source organism: Mus musculus
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8VDF2 (Residues: 404-613; Coverage: 27%)
Gene names: Np95, Uhrf1
Sequence domains: SAD/SRA domain
Structure domains: SRA-YDG
DNA (5'-D(*DCP*DTP*DAP*DCP*DCP*DGP*DGP*DAP*DTP*DTP*DGP*DC)-3') Chain: C
Molecule details ›
Chain: C
Length: 12 nucleotides
Theoretical weight: 3.64 KDa
Source organism: Mus musculus
Expression system: Not provided
DNA (5'-D(*DGP*DCP*DAP*DAP*DTP*DCP*(5CM)P*DGP*DGP*DTP*DAP*DG)-3') Chain: D
Molecule details ›
Chain: D
Length: 12 nucleotides
Theoretical weight: 3.7 KDa
Source organism: Mus musculus
Expression system: Not provided

Ligands and Environments

No bound ligands
1 modified residue:
Ligand 5CM 1 x 5CM

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: P41212
Unit cell:
a: 59.081Å b: 59.081Å c: 193.971Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.221 0.219 0.275
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

89 review citations

Establishing, maintaining and modifying DNA methylation patterns in plants and animals.
Law et al. (2010)
88 more

2 mentions without citation

Structure-guided sequence specificity engineering of the modification-dependent restriction endonuclease LpnPI.
Sasnauskas et al. (2015)
1 more